I wired my own harness from scratch, basically. When I bought an '03 3L back in '05, The engine came with a pristine harness. Since it was meant for a Taurus and wouldn't fit as it was, I cut it apart, and used all the connectors as pig-tails, and wired it up to the 2.5L PCM connector. It was a lot of splices, but solder+weather proof heatshrink makes it a non-issue. My harness worked first try, and never failed. (I worked in custom 12v shops as a kid, and this job was no sweat for me. You'll do fine wiring your own.
My advice:
Trace out the factory harness, record PCM pin location/wirecolor/function(or connector) before you cut ANYTHING apart.
Never use bell caps, butt connectors, or scotch locks for splices. Solder only!
Make sure to keep the shielded wires shielded (Crank/Cam sensors, etc.).
If you want a harness that will last forever... Get some nice silicone aviation wiring ($$!), and new crimp-on pins for each of the connectors(PCM pins are hard to find, but are available). It will last forever this way, assuming you use the correct crimp tool, and proper wire size.